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PMID: 17351000 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Biophysical journal ·Vol. 92 ·No. 11 ·2007-06-01 ·Pages 3817-29

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M

Abstract

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution.

MeSH Terms
Computer Simulation DNA/chemistry Models, Molecular Nucleic Acid Conformation RNA/chemistry
Chemicals
RNA DNA
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Pérez Alberto
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica & Instituto Nacional de Bioinformática, Parc Científic de Barcelona, Barcelona 08028, Spain.
Marchán Iván
Svozil Daniel
Sponer Jiri
Cheatham Thomas E
Laughton Charles A
Orozco Modesto
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Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
0006-3495
DOI
10.1529/biophysj.106.097782
Published
2007-06-01
Epub
2007-00-09
Pages
3817-29
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC1868997
Subset
IM
External Links
PubMed source DOI: 10.1529/biophysj.106.097782 PMC Full Text View journal details
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